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- PDB-3flh: Crystal structure of lp_1913 protein from Lactobacillus plantarum... -

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Basic information

Entry
Database: PDB / ID: 3flh
TitleCrystal structure of lp_1913 protein from Lactobacillus plantarum,Northeast Structural Genomics Consortium Target LpR140B
Componentsuncharacterized protein lp_1913
Keywordsstructural genomics / unknown function / alpha-beta protein / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homology
Function and homology information


Rhodanese-like domain / Oxidized Rhodanese; domain 1 / Rhodanese Homology Domain / Rhodanese-like domain / Rhodanese domain profile. / Rhodanese-like domain superfamily / Rhodanese-like domain / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
BROMIDE ION / Rhodanese domain-containing protein / :
Similarity search - Component
Biological speciesLactobacillus plantarum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsSeetharaman, J. / Chen, Y. / Forouhar, F. / Sahdev, S. / Foote, E.L. / Ciccosanti, C. / Belote, R.L. / Everett, J.K. / Nair, R. / Acton, T.B. ...Seetharaman, J. / Chen, Y. / Forouhar, F. / Sahdev, S. / Foote, E.L. / Ciccosanti, C. / Belote, R.L. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal structure of lp_1913 protein from Lactobacillus plantarum,Northeast Structural Genomics Consortium Target LpR140B
Authors: Seetharaman, J. / Chen, Y. / Forouhar, F. / Sahdev, S. / Foote, E.L. / Ciccosanti, C. / Belote, R.L. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. / Montelione, G.T. / Hunt, J.F. / Tong, L.
History
DepositionDec 18, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 13, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: uncharacterized protein lp_1913
B: uncharacterized protein lp_1913
C: uncharacterized protein lp_1913
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,8174
Polymers41,7373
Non-polymers801
Water3,783210
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4290 Å2
ΔGint-40 kcal/mol
Surface area16640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.892, 47.429, 62.769
Angle α, β, γ (deg.)90.00, 113.55, 90.00
Int Tables number4
Space group name H-MP1211
Detailstrimer

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Components

#1: Protein uncharacterized protein lp_1913


Mass: 13912.362 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus plantarum (bacteria) / Strain: WCFS1 / Gene: lp_1913 / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic / References: UniProt: Q88VW8, UniProt: F9UPN6*PLUS
#2: Chemical ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Br
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 210 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.89 Å3/Da / Density % sol: 35.01 %
Crystal growTemperature: 293 K / pH: 7.5
Details: Protein solution: 10 mM Tris (pH 7.5), 100 mM sodium chloride, and 5 mM DTT. Reservoir solution: 100 mM sodium acetate (pH 5.0), 40% PEG 4k, and 100 mM sodium bromide. Microbatch under oil, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.97892 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Dec 2, 2008 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97892 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. all: 41490 / Num. obs: 41366 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 7.4 Å2 / Rmerge(I) obs: 0.103 / Rsym value: 0.098 / Net I/σ(I): 16.52
Reflection shellResolution: 2→2.07 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.371 / Mean I/σ(I) obs: 4.5 / Num. unique all: 4186 / Rsym value: 0.529 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SHELXthen SOLVE/RESOLVEmodel building
CNS1.2 & XtalViewrefinement
HKL-2000data reduction
SCALEPACKdata scaling
SHELXthen SOLVE/RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2→19.88 Å / Rfactor Rfree error: 0.006 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.248 1857 5 %RANDOM
Rwork0.193 ---
all0.196 41379 --
obs0.195 37117 89.7 %-
Displacement parametersBiso mean: 23.9 Å2
Baniso -1Baniso -2Baniso -3
1--1.81 Å20 Å2-2.73 Å2
2--4.96 Å20 Å2
3----3.16 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.21 Å0.13 Å
Refinement stepCycle: LAST / Resolution: 2→19.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2584 0 1 210 2795
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.006
X-RAY DIFFRACTIONo_angle_deg1.1
X-RAY DIFFRACTIONo_dihedral_angle_d22.2
X-RAY DIFFRACTIONo_improper_angle_d0.67
LS refinement shellResolution: 2→2.07 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.275 153 5.1 %
Rwork0.19 2874 -
obs-2874 72.5 %

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